This folder contains the model independent stuff plus some
place holders for PLA4 models.



Model specific files  to be added

Ops files -- name as you like
  Each kind of op in a separate module 
  Usually in separate file in the Ops directory
Rules files -- you can use one rules file or make a Rules directly
and have several files.

all.maude -- loads the model files (ops and rules)
and defines the top-level modules [edit template as needed
according to the ops and rule module names]

theops.maude  -- is now the same for all models 
  If we need to expand in the future we can.

input.txt -- for debugging -- you probably don't want to mess with this.
  
componentJInfoSpec.json --- specifies what metadata is displayed
  for occurrences and how.  The place holder comes from TinyKB

evidence.txt --- could be empty -- specifies rule to evidence map

Configuration files -- these tell maude what to load and how to initialize
load-jpl-fresh.maude  
load-jpl-restore.maude
load-jpl-fresh-all.maude  
load-jpl-restore-all.maude

fresh[-all] regernerates the knowledge base (tkb,-graph,-occmap files)
and the JSON description.  Without -all only the ops that are actually
used in a rule occurrence are considered.  With -all all the declared
ops are included.  The latter is mainly useful when we want to
edit rules on the fly, as it provides an extended vocabulary.

restort [-all] just loads the saved kb (maude and json).
Use this unless you have edited the maude since the last fresh.

In the load files for your model you will need to edit as follows:
1. uncomment the appropriate evidence path expression (or define a new one)
2.  In fresh [-all] in the line following *** initialize viewer kb
   replace PROTEINOPS CHEMICALOPS GENEOPS by a list of names of modules
   in your Ops folder.  Note that LOCATIONOPS and MODIFICATIONOPS are
   added by maude, no need to list them explicitly
   

Pointing iop to the corresponding configuration file
startup-jfresh-all.txt
startup-jfresh.txt
startup-jrestore-all.txt
startup-jrestore.txt
startup.txt -- defaults to startup-jrestore.txt -- edit to pick your default

CAVEAT  after load-jpl-fresh[-all] -- check JSON/baseOps.json for 
badstr -- that flags declarations with ill-formed metadata.
Fix the offending metadata and try again. 
OW starting up the system may fail in obscure ways.
